Warnings when using coverageToExon()
lcolladotor opened this issue · comments
Hm... I don't know how to deal with this warning. Specially since running the coverageToExon() code manually (that is, looping manually instead of using mclapply) does not reproduce the warnings. It could be a NAMESPACE issue.
I'll most likely need help from the Bioc-devel mailing list.
Anyhow, here are the warnings:
> example("coverageToExon", "derfinder")
cvrgTE> ## Obtain fullCov object
cvrgTE> fullCov <- list("21"=genomeDataRaw$coverage)
cvrgTE> ## Use only the first two exons
cvrgTE> smallGenomicState <- genomicState
cvrgTE> smallGenomicState$fullGenome <- smallGenomicState$fullGenome[ which(smallGenomicState$fullGenome$theRegion == "exon")[1:2] ]
cvrgTE> ## Finally, get the coverage information for each exon
cvrgTE> exonCov <- coverageToExon(fullCov=fullCov, genomicState=smallGenomicState, L=100)
2014-04-14 15:21:55 coverageToExon: processing chromosome 21
Warning messages:
1: In (function () :
Symbol 'cc' resolved from calling frame; escape with .(cc) for safety.
2: In (function () :
Symbol 'chr' resolved from calling frame; escape with .(chr) for safety.
> options(warn=2)
> example("coverageToExon", "derfinder")
cvrgTE> ## Obtain fullCov object
cvrgTE> fullCov <- list("21"=genomeDataRaw$coverage)
cvrgTE> ## Use only the first two exons
cvrgTE> smallGenomicState <- genomicState
cvrgTE> smallGenomicState$fullGenome <- smallGenomicState$fullGenome[ which(smallGenomicState$fullGenome$theRegion == "exon")[1:2] ]
cvrgTE> ## Finally, get the coverage information for each exon
cvrgTE> exonCov <- coverageToExon(fullCov=fullCov, genomicState=smallGenomicState, L=100)
2014-04-14 15:22:04 coverageToExon: processing chromosome 21
Error in (function () :
(converted from warning) Symbol 'cc' resolved from calling frame; escape with .(cc) for safety.
> traceback()
27: doWithOneRestart(return(expr), restart)
26: withOneRestart(expr, restarts[[1L]])
25: withRestarts({
.Internal(.signalCondition(simpleWarning(msg, call), msg,
call))
.Internal(.dfltWarn(msg, call))
}, muffleWarning = function() NULL)
24: .signalSimpleWarning("Symbol 'cc' resolved from calling frame; escape with .(cc) for safety.",
quote((function ()
{
val <- get(g, enclos)
warning("Symbol '", g, "' resolved from calling frame; ",
"escape with .(", g, ") for safety.")
val
})()))
23: warning("Symbol '", g, "' resolved from calling frame; ", "escape with .(",
g, ") for safety.")
22: (function ()
{
val <- get(g, enclos)
warning("Symbol '", g, "' resolved from calling frame; ",
"escape with .(", g, ") for safety.")
val
})()
21: eval(expr, envir, enclos)
20: eval(expr, as.env(envir, enclos))
19: eval(expr, as.env(envir, enclos))
18: eval(expr, envir, enclos)
17: eval(expr, envir, enclos)
16: safeEval(substitute(subset), x, top_prenv(subset))
15: .local(x, ...)
14: subset(fullCov[[chrnum]], cc[[chr]])
13: subset(fullCov[[chrnum]], cc[[chr]])
12: FUN(1L[[1L]], ...)
11: lapply(X = X, FUN = FUN, ...)
10: mclapply(seq(along = fullCov), .coverageToExonChrStep, fullCov = fullCov,
cc = cc, e = e, L = L, verbose = verbose, mc.cores = nCores)
9: FUN(X[[1L]], ...)
8: lapply(X = X, FUN = FUN, ...)
7: mclapply(strandIndexes, .coverageToExonStrandStep, fullCov = fullCov,
etab = etab, L = L, nCores = nCores, verbose = verbose, mc.cores = nCores)
6: coverageToExon(fullCov = fullCov, genomicState = smallGenomicState,
L = 100) at Rex148844c31d37e#15
5: eval(expr, envir, enclos)
4: eval(ei, envir)
3: withVisible(eval(ei, envir))
2: source(tf, local, echo = echo, prompt.echo = paste0(prompt.prefix,
getOption("prompt")), continue.echo = paste0(prompt.prefix,
getOption("continue")), verbose = verbose, max.deparse.length = Inf,
encoding = "UTF-8", skip.echo = skips, keep.source = TRUE)
1: example("coverageToExon", "derfinder")
> sessionInfo()
R version 3.1.0 (2014-04-10)
Platform: x86_64-apple-darwin10.8.0 (64-bit)
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] derfinder_0.0.53
loaded via a namespace (and not attached):
[1] AnnotationDbi_1.25.18 BatchJobs_1.2 BBmisc_1.5 Biobase_2.23.6
[5] BiocGenerics_0.9.3 BiocParallel_0.5.20 biomaRt_2.19.3 Biostrings_2.31.22
[9] biovizBase_1.11.15 bitops_1.0-6 brew_1.0-6 BSgenome_1.31.13
[13] bumphunter_1.3.8 cluster_1.15.2 codetools_0.2-8 colorspace_1.2-4
[17] DBI_0.2-7 dichromat_2.0-0 digest_0.6.4 doRNG_1.5.5
[21] fail_1.2 foreach_1.4.1 Formula_1.1-1 GenomeInfoDb_0.99.31
[25] GenomicAlignments_0.99.38 GenomicFeatures_1.15.15 GenomicRanges_1.15.44 ggbio_1.11.16
[29] ggplot2_0.9.3.1 grid_3.1.0 gridExtra_0.9.1 gtable_0.1.2
[33] Hmisc_3.14-3 IRanges_1.21.45 iterators_1.0.6 labeling_0.2
[37] lattice_0.20-29 latticeExtra_0.6-26 locfit_1.5-9.1 MASS_7.3-31
[41] matrixStats_0.8.14 munsell_0.4.2 parallel_3.1.0 pkgmaker_0.20
[45] plyr_1.8.1 proto_0.3-10 qvalue_1.37.3 R.methodsS3_1.6.1
[49] RColorBrewer_1.0-5 Rcpp_0.11.1 RCurl_1.95-4.1 registry_0.2
[53] reshape2_1.2.2 rngtools_1.2.4 Rsamtools_1.15.41 RSQLite_0.11.4
[57] rtracklayer_1.23.22 scales_0.2.3 sendmailR_1.1-2 splines_3.1.0
[61] stats4_3.1.0 stringr_0.6.2 survival_2.37-7 tcltk_3.1.0
[65] tools_3.1.0 VariantAnnotation_1.9.51 XML_3.98-1.1 xtable_1.7-3
[69] XVector_0.3.7 zlibbioc_1.9.0
>